System and method for incubation and reading of biological cultures

ABSTRACT

The present invention describes an integrated incubator and image capture module that regulates the incubator atmosphere and obtains high-resolution digital images of sample specimens. The incubator has a cabinet type enclosure that enables the provision of a controlled environment to the contents of the incubator by having at least three ports on one face of the cabinet for the passage of sample containers. Additionally, an image capture module is located immediately adjacent to the incubator. In this regard, using at least three separate access/egress points for the sample containers streamlines operation of the system and enhances preservation of the incubator environment. Furthermore, locating the image capture module directly adjacent to the incubator reduces the amount of time a sample container is exposed to the external environment, thereby reducing the extent to which samples are exposed to potential contaminants and reducing the exchange of the lab and ambient atmospheres.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of the filing date of U.S.Provisional Patent Application No. 61/980,272 filed Apr. 16, 2014, thedisclosure of which is hereby incorporated herein by reference.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates to a method and system for incubating andanalyzing biological samples.

Description of the Related Art

Sample incubators are used to grow and maintain microbiological and cellcultures prepared from biological samples for research and analysis in anumber of fields. The simplest incubators are insulated boxes that workby controlling a number of environmental factors, including temperatureand humidity to provide an environment suitable to maintain sampleviability and/or to support microbial growth. Incubators also havefeatures that control the composition of the atmosphere in theincubator, such as the amount of carbon dioxide and/or oxygen in theincubator environment.

One problem with incubators is the difficulty in maintaining thecontrolled atmosphere when samples are retrieved from the incubator.Typically, containers that contain growth media inoculated with samplesuch as, e.g., petri dishes, have a culture media that providesnutrients that support microbial growth therein. In addition to thenutrients, the media often has other additives (e.g. sodium chloride)that will provide the culture media with the correct consistency tosupport the growth of target microorganisms, or nutrient indicators thatwill indicate target microorganisms, if present in the sample. Onechallenge for incubators with controlled atmospheres is maintaining thecontrolled atmosphere when the sample is inserted, removed from orreplaced into the incubator as the sample is evaluated to determine thepresence of absence of microorganisms in the sample.

In a simple incubator, a single door or hatch located on one side, orthe top, of the incubator enclosure is provided to access the contentsof the incubator, either to place samples in the incubator or removethem therefrom. This results in a significant loss of the incubator'scontrolled atmosphere to the larger environment, typically a laboratoryenvironment, in which the incubator is placed. Also, opening the doorallows the ambient atmosphere to enter the incubator. The loss of thecontrolled environment in the incubator enclosure can retard microbialgrowth in the culture media or contaminate the specimen.

Additionally, removing the sample containers from the incubator for anextended period of time, for example to electronically image the sampleculture to detect microbial growth, could negatively impact the growthof the target microorganisms or expose the specimens to contaminants inthe lab, which can adversely affect the integrity of the assay results.

One example of a commercially available system for incubation andimaging is the BD Kiestra™ ReadA™. The BD Kiestra™ ReadA™ system uses aseries of tracks to move plates within the incubator. During and afterincubation, the plates are removed and are optionally inspected byoptical imaging for evidence of microbial growth. The images of theplates taken during incubation are compared to determine growth results.

Thus, there is a need in the art for systems that provide monitoringcapabilities for cultures under incubation that maintain the integrityof the incubator's controlled atmosphere and reduce the amount of time aspecimen being incubated/cultured is exposed to lab conditions withlittle to no operator intervention. Furthermore, there is a need to moreefficiently manage the flow of plated cultures into and out of theincubator yet preserve the controlled environment in the incubator asplated cultures are placed in and removed from the incubator forprocessing.

BRIEF SUMMARY OF THE INVENTION

The present invention addresses the above problems by providing anintelligent incubation and imaging system that combines regulating theincubator atmosphere with automatic, high-resolution digital imaging.Moreover, the combined incubator and imaging system described in thecurrent application can fit seamlessly into an automated lab environmentor be a stand-alone unit working with a lab operator.

The incubator has a cabinet type enclosure that enables the provision ofa controlled environment to the contents of the incubator. Typically,the contents of the incubator are containers such as petri dishes thatcontain nutrient media that has been inoculated by a biological orenvironmental sample. The nutrient media and controlled atmosphereprovided to the incubator support the growth of at least certainmicrobes in the media if present in the sample with which the media hasbeen inoculated.

Structurally, one face of the incubator has hatches or doors locatedthereon as dedicated ports for automated placement and removal ofsamples from the incubator cabinet. Typically, the incubator cabinet hasmultiple ports to facilitate ingress and egress of petri dishes into andout of the cabinet. In one embodiment described herein the cabinet hasat least three such ports, preferably all located on the same side ofthe cabinet (referred to as the first face of the cabinet). These portsare referred to as doors herein to reflect the fact that the ports openand close to preserve the cabinet environment as the petri dishes enterinto or are removed from the cabinet. According to some embodiments,each door may include separate ports for ingress and egress of thesample containers. In other embodiments, a port may have more than onedoor for ingress and egress of the sample containers. Doors, as usedherein, are one example of a port that will open to allow an article,such as a sample container, to be conveyed through the door and closeafter such passage.

In certain embodiments the ports are configured as doors., The firstport may be a door dedicated to accepting automated delivery of samplecontainers (e.g. petri dishes) into the incubator cabinet. As such, thesamples are conveyed to the door, which opens when a sensor indicatesthe presence of a container to be transported into the cabinet. In oneembodiment, the sensor communicates the presence of the sample containerto a processor, which then communicates with the door actuator. The dooropens automatically and the sample is transferred from the externalconveyer to an internal apparatus that places the sample container in alocation within the incubator that is associated with the sample.Software is used to track the placement of the sample in the incubator,the sample container having a machine readable tag (e.g. a barcode, RFIDtag, label, etc.) that enables the location of the sample in theincubator to be known at all times using a reader for that tag and arobotic mechanism for the controlled placement and retrieval of thesample containers in the incubator environment. Conveyers and roboticmechanisms for controlled movement and placement of sample containers iswell known to one skilled in the art and not described in detail herein.

The second port or door may be a dedicated door through which samplecontainers are finally removed from the incubator. By final removal itis meant that the system has determined that the residence time of thesample in the incubator has ended, where such end-point may be based onexpiration of an incubation time or may be based on feedback from theimaging process unit detailed below. Upon removal, the samples may bemoved to disposal (e.g., if no growth has occurred) , may be retrievedby an operator, or maybe moved in an automated manner to a downstreamanalysis module or instrument.

The third port or door may be a dedicated single door to an automatedelectronic image capture module or it can be multiple ports or doors. Asnoted above, the third port may include individual ports for ingress andegress of the sample containers. For example, the third door may includea dual door construction that includes a first door through which samplecontainers enter the image capture module and a second door throughwhich sample containers exit the image capture module. Accordingly, theimage capture module may receive samples from the incubator forinspection to ascertain if the sample has changed over time, e.g. ifmicrobial growth has occurred in the sample. The module is enclosed andsample containers are transported directly into the module from thecabinet and are directly returned to the cabinet using a conveyerdisposed in the image capture module.

In one embodiment, the incubator also includes a robotic arm forhandling and moving the one or more containers amongst the three doorsof the incubator and within the incubator itself. By using such arobotic arm, in particular in combination with the automated conveyorsystems and the automated in-feed conveyor, the throughput of cellculture devices can be increased even further. Preferably, the incubatorincludes a plurality of positions (i.e. slots or shelving).

In an alternate embodiment, the incubator may also include a wasteremoval station that includes a waste removal outlet separate from thethree doors in the face of the incubator. In this regard, the wasteremoval station includes a waste transportation element for transportinga container marked for removal to the waste removal station via thewaste removal outlet. By providing a separate waste removal outlet theremoval of the waste containers from the incubator can be performed suchthat it does not interfere with the discharge of useful containers fromthe incubator via the second door. In this regard, the throughput ofcontainers is increased even further. In addition by providing aseparate waste removal outlet the removal of containers from theincubator can reduce the risk of incubator contamination andcontamination of other specimen containers. Additionally, the wasteremoval outlet helps to maintain the controlled environmental conditionswithin the incubator.

The image capture module is an enclosed unit immediately adjacent to theincubator. This enables direct transport of the sample from theincubator into the environment of the image capture module with notransport through one or more intervening environments. As noted above,sample containers, such as petri dishes, are conveyed into the imagecapture module through the third port, or an ingress door of the thirdport. Thereafter, a lid of the sample container may be removed such thatan image capture unit may electronically image (e.g. digitallyphotographs) the sample container. The lid may be replaced after thesample container has been imaged and the sample container may beconveyed back through the same third door, or alternatively through anegress door of the third port, for placement back into the controlledincubator environment to continue incubation.

Having at least three separate access/egress points for the samplecontainers to enter into and be removed from the incubator cabinetprovides many advantages to automated incubator operation. Examples ofsuch advantages include streamlined operation due to separate conveyortracks for separate functions, enhanced preservation of incubatorenvironment because the amount of time any single door is open to theexternal environment is reduced compared with configurations with fewerdoors and comparable capacity and functionality. Moreover, having theimage capture module directly adjacent to the incubator reduces theamount of time the sample container is exposed to an externalenvironment (with its lack of precisely controlled temperature andatmosphere and potential contaminants) while the sample container isimaged. Since the image capture module is enclosed, it acts as a shieldbetween the lab atmosphere and the incubator atmosphere reducing theextent to which the lab atmosphere enters the incubator and the samplecontainers enter from the incubator and return thereto through the thirddoor.

Further advantages will be realized by various aspects of the inventionand will be apparent from the following detailed description. One of theadvantages of the system described herein is the integration withautomated platforms for plate inoculation, providing end-to-endautomation for inoculation of sample onto plated media, streaking ofsample on to media and incubation of inoculated media for growth oftarget microorganisms. The present system is flexible and can alsohandle plated media that have been inoculated manually.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention will be better understood from the Detailed Description ofthe Preferred Embodiments and from the appended drawings, which aremeant to illustrate and not to limit the invention, and wherein:

FIG. 1 is a perspective view of a system for automated management andprocessing of containers for culture growth;

FIGS. 2A and 2B are cross-sectional views of different embodiments ofthe schematic representation of FIG. 1;

FIG. 3 is an exemplary screen shot for the image capturing and analysisof the captured images;

FIG. 4 is an incubator cabinet integrated with external conveyors,stackers, and an image capture module;

FIGS. 5A and 5B illustrate the waste removal outlet station according toone embodiment of the present invention;

FIG. 6 is a schematic of the robotic arm used to manage the containers;

FIG. 7A is a front view of the integrated incubator and image capturemodule with external conveyors shown in the foreground;

FIG. 7B is a side view of the external conveyors and an image capturemodule with a portion of the incubator cut away to reveal the portionsof the conveyors that extend into the incubator cabinet;

FIG. 8 is a perspective view of a conveyor portion that permits petridishes to be automatically conveyed out of the incubator cabinet througha door disposed in the cabinet housing;

FIG. 9 is a perspective view of a conveyor portion with a stackingconveyor system for moving petri dishes into the incubator and stackingthem for further handling;

FIG. 10 is an exterior perspective view of the housing of the imagecapture module;

FIG. 11 is a perspective view of an interior portion of the imagecapture module which illustrates the conveyor from the incubatingsystem, through the imaging unit and back to the incubator;

FIGS. 12A and 12B are cut away top plan views of the image capturemodule;

FIG. 13 is an illustration of a lid manipulator unit;

FIG. 14 is a bottom perspective view of the conveyor in the imagecapture module illustrating a mechanism that moves the petri dish intoposition for image capture;

FIG. 15 is a cut away side view of one embodiment of the image capturecomponent of the imaging unit; and

FIG. 16 is a top down view of a light source disposed above the petridish containers for the image capture unit according to an embodiment ofthe present invention.

DETAILED DESCRIPTION

FIGS. 1, 2A, and 2B illustrate a perspective view and schematicrepresentation of different embodiments of a system 1 for automatedmanagement of sample containers such as plated media according to thepresent invention is shown. The system 1 includes at least oneintegrated incubator and image capture module 3. The integratedincubator and image capture module 3 includes a housing having anincubation chamber 5 that controls environmental conditions such thatinoculated containers 2 can be cultured in a controlled manner. Theintegrated incubator and image capture module 3 as illustrated in FIGS.1 and 2 also includes a loading station 6 having a first door 7 forreceiving inoculated containers 2 a into the incubation chamber 5. Inthe illustrated embodiment, a discharge station 8 having a second door 9separate from the first door 7 is provided to allow for the discharge ofincubated inoculated containers 2 b from the incubation chamber 5.

As seen from the embodiment shown in FIGS. 1 and 2, the first door 7 andthe second door 9 are provided on the same side of the incubationchamber 5. A discharge door 9 is located on the housing, opposite thefirst door 7. In alternative embodiments, different locations for thefirst, second and third doors and the discharge door are contemplated.

In the illustrated embodiment, the first door 7 and the discharge door 9are closable. In this embodiment, a microprocessor 10 controls dooroperation. However, alternative embodiments may include a sensorproximately located to the door to control the opening and closing ofthe doors located on the housing 4.

As noted above, in described embodiments the integrated incubator andimage capture module 3 has a microprocessor 10 that controls functionsand allows for programmable operation of all the components of theintegrated incubator and image capture module 3. In the illustratedembodiments, the microprocessor 10 is provided within the housing 4 asillustrated in FIGS. 1 and 2. However, one of ordinary skill in the artwill recognize that the microprocessor 10 may be external to the housing4 and control the integrated incubator and image capturing module 3 viaa data link, such as a direct connection (i.e., USB), a wirelessconnection, or over a network.

In the illustrated embodiments, the system 1 for automated management ofcontainers 2 includes at least one evaluation station 11. Asillustrated, the system 1 may have a plurality of evaluation stations11. The evaluation stations 11 are located remotely from the integratedincubator and image capture module 3.

In this regard, an automated transfer conveyor 12 conveys the incubatedinoculated containers 2 b from the discharge station 8 of the integratedincubator and image capture module 3 to the evaluation stations 11. Atransfer conveyor controller 13 is provided to control the operations ofthe transfer conveyor 12. In this regard, the transfer conveyorcontroller 13 advantageously communicates with relevant components ofthe system 1 via an interface 14.

In the illustrated embodiments, the system 1 further comprises anautomated in-feed conveyor 15 for transporting inoculated contains 2 ato the loading station 6 of the integrated incubator and image capturemodule 3. An in-feed conveyor controller 16 communicates with thein-feed conveyor 15 and the various components of the system 1 via aninterface 17.

Referencing FIG. 2A, the integrated incubator and image capture unit 3includes a storage array 18 within the housing 4 for accommodating aplurality of inoculated containers 2. Preferably, the storage array 18is partially cylindrical and defines a virtual vertical axis 19. Thehousing 4 may include a plurality of the storage arrays 18 arrangedalong its interior walls. Typically, the housing includes between 500and 2000 positions (i.e., slots or shelving) each adapted to receive andhold an inoculated container 2. In some embodiments, each position ofthe plurality of positions of the storage array 18 includes a coordinaterepresentative of that position to distinguish from other positions. Thestorage array will be discussed further with respect to FIG. 5A.

In the illustrated embodiment, a robotic arm 20 is mounted within thehousing 4 for handling and moving containers 2 from the first door 7 toone of the plurality of positions. Additionally, the robotic arm 20 maymove a container 2 from a position to the second door 9 and, ifnecessary, between different positions of the storage array 18. Therobotic arm 20 will be discussed in greater detail with respect to FIGS.5B and 6.

In operation, the robotic arm 20 is configured to move in a directionalong an axis 21, which is parallel to the vertical central axis 19. Therobotic arm 20 includes a mechanical gripper 22 and a translational arm23. The gripper 22 is mounted on the translational arm 23 by atranslational joint 24. Alternatively, multiple translational joints maybe used. For example, as illustrated in FIG. 6, the gripper 22 ismounted to the translational arm 23 by a translational joint 24 thatmoves the gripper 360°. The translational arm 23 may also include anadditional translational joint to move the gripper in the vertical axis.One of ordinary skill in the art would recognize that the range ofmotion of the gripper function is a design choice and the variousconfigurations would be readily apparent by the embodiments describedherein.

In the illustrated embodiment, the system 1 further comprises amechanism for tracking containers within the system 1. Each container 2may include identification information or code 25 for identifying aspecific container 2. Such an identification code 25 may include alabel, a bar code, a number, a series of numbers, a color, a series ofcolors, a letter, a series of letters, a symbol, a series of symbols, anRFID tag, a NFC chip, or any combination thereof.

The identification code 25 may be read by a plurality of readers 26positioned at strategic positions within the system 1. In this regard,the identification code 25 is advantageously used to track (e.g., one ormore of locating, identifying, identifying the position of as relativeto a point of origin, or cataloging (keeping a record of)) the container2. The identification code 25 of each container 2 in the system 1 isunique to the container bearing the identification code. Thus, everycontainer in the automated container management system 1 may bedistinguished from other containers. In some embodiments, the mechanismfor tracking containers 2 may include one or more position sensors 27,placed in the incubation chamber 5 that may be used to correlate aspecific coordinate with a specific position within the incubationchamber 5.

In some embodiments, the integrated incubator and image capture module 3includes an image capture module 200 configured to capture an image of acontainer 2. According to this embodiment, the microprocessor 10 mayissue a command for obtaining an image of a container. Themicroprocessor 10 causes the robotic arm 20 to pick up the container 2from its position within the storage array 18. After removing thecontainer 2 from its position, the robotic arm 20 places it on shelf 220(FIG. 7B) so that the image capture module 200 may obtain an image ofsaid container 2. The image capture module 200 is described in greaterdetail below.

The obtained image can be outputted via a line 29 and an interface 30 toan evaluation station 11. As illustrated, the line and interface areshown external to the image capture module 200. Further, one of ordinaryskill in the art would recognize that the interface 30 may be internalto the image capture module 200. Further, one of ordinary skill in theart would also recognize that the line 29 may be any type of data link,wired or wireless, used to communicate the captured image to theevaluation station 11.

Alternatively, as shown in FIG. 2B the image capture module 200 may belocated inside the housing 4 of the integrated incubator and imagecapture module 3. According to this embodiment, the microprocessor 10issues a command for obtaining an image of a container. Themicroprocessor 10 controls the robotic arm 20 such that a container ispicked up from its position within the storage array 18. The robotic arm20 then moves the container to the image obtaining device 28 forobtaining an image of said container. The obtained image may beoutputted via a line 29 and an interface 30 to an evaluation station 11.As discussed above, the evaluation station 11 includes an interface 31and a display device 32 for receiving and displaying the outputted imageof the container.

As noted above, the evaluation station 11 may include an interface 31and a display device 32 connected to the image capture device 200 forreceiving and displaying the outputted image of the container 2.

In some embodiments, the evaluation stations 11 may include a taggingdevice. The tagging device is operatively connected to themicroprocessor 10 of the intelligent incubator and image capture module3. According to this embodiment, a tagging device is formed by an inputdevice 33 at each evaluation station 11. In this regard, the inputdevice 33 may be directly connected to the microprocessor 10 orindirectly connected to the microprocessor 10 via a central systemcontrol computer 34. The input device 33 may typically be a key board, acomputer mouse, a track ball, a touch screen display, or any other knowndevice capable of making a mark.

Turning to FIG. 3, an example of associating a tag with a container 2 isshown. Typically, an image of the container is displayed on the display32. Typically, the display 32 shows images of four containers 2 ai, 2aj, 2 ak, 2 al. One of ordinary skill in the art will recognize that thenumber of containers shown on display 32 is a design choice. In thisregard, one of ordinary skill in the art would recognize that more orfewer images of containers may be shown on display 32.

For each container displayed on the display 32 of FIG. 3, a number ofwindows are displayed containing additional information related to thesample. For example, information regarding the identity of the container(i.e., indicated by the box “Barcode”), the date (and optionally thetime) on which the container was placed in the incubation chamber 5(indicated by the box “Date”) may be displayed to the lab operator.Certain information, such as the Barcode and Date information, cannot bechanged by an operator, and are instead updated by the automatedcontainer management system 1.

In some embodiments, other operational boxes may be displayed which mayindicate further processing to be performed on the particular container2. For example, the operations “Call up,” “Leave,” “Scan,” and “Waste”are available to the lab operator. By moving the input device 33 to oneof these additional operational box and choosing the operation mentionedtherein (i.e., clicking or marking the box), the particular container 2is tagged and data indicating the tag is sent to the microprocessor (orcentral system control computer 34). The system then performs theselected operation on the container 2 automatically.

For example, if the container 2 ai is tagged with the operation Scan,the robotic arm 20 moves the container 2 ai to the reader 26 within theincubation chamber 5 to confirm the identity of the container.Additionally, when the operation Call up is selected for the container 2aj, the container 2 aj is moved by the robotic arm 20 towards thedischarge station 8, and is subsequently transported out of theincubation chamber 5 via the second door 9. The container 2 aj may betransported to an evaluation station 11 where the tagging was performedvia the automated transfer conveyor 12.

In another example, the container 2 ak is tagged with the operationLeave, then the container 2 ak is to remain in the incubation chamber 5.Optionally, when the Leave operational box is selected, a new window maypop-up to indicate a number of choices for the additional time thecontainer 2 ak is to remain in the incubation chamber 5. Further, thedisplay 32 may have a pop-up window that allows the lab operator to setthe expiry time of the container 2 ak. At the expiry time, the roboticarm 20 moves the container 2 ak to the image obtaining device 28 toobtain a new image of the container. The captured image is typicallydisplayed on a display 32 of an evaluation station 11.

Referring to the container 2 a 1, the Waste tag is selected. Accordingto this option, a signal is sent to the microprocessor 10 which isarranged for controlling the integrated incubator and image capturemodule 3 to remove the container 2 a 1. According to some embodiments,the container 2 a 1 may be discharged via the second door 9 and removedfrom the system 1 by a separate sorting unit (not shown). Alternatively,the container 2 a 1 may be removed from the incubator via a wasteremoval outlet 35, separate from the three doors in the face of theincubator. The waste removal outlet 35 may connect to a waste removalstation 36 separate from the incubation chamber 5.

One of ordinary skill in the art would recognize that the layout of thedisplay 32 may be altered to suit the needs of the individual laboperators. Arranging different layouts is well known to those skilled inthe art and will not be discussed in greater detail herein.Additionally, the operations set forth above are merely illustrative,and one of ordinary skill in the art would recognize that differentoptions may be presented to the lab operator for further processing ofthe containers 2.

As discussed above and shown in FIG. 1, a waste removal outlet 35 may beincluded in incubation chamber 5 that is separate from both the seconddoor 9 and the first door 7. In this regard, the waste removal outlet 35may provide an alternative for removing waste containers from theincubation chamber 5, thereby reducing interference with thetransportation operations of other containers into and out of theincubation chamber 5.

FIG. 4 illustrates another embodiment of the integrated incubator andimage capture module 3. The integrated incubator and image capturemodule 3 includes the incubator 100, an image capture module 200, and afirst track system 300 that receives specimens for incubation andtransports them into the incubator. A second track system 400 transportscontainers inoculated with sample from the incubator whenincubation/imaging is complete. Conveyor 300 is equipped with racks orcassettes that can receive petri dishes and hold them in a stack.

In preferred embodiments, the integrated incubator and image capturemodule 3 is capable of being integrated into a fully automatedlaboratory environment. In this regard, containers such as plates, e.g.petri dishes (illustrated), having culture media inoculated withbiological fluids such as blood, urine, sputum, etc. or other biologicalor environmental samples for incubation and inspection are received onthe first track 300. Suitable sample containers are well known to oneskilled in the art and are not described in detail herein. Neither areculture media or types of samples used to inoculate the culture media.In the automated laboratory environment, there can be several integratedincubator and image capture modules, each incubator having, for example,different atmospheric conditions and settings. The first track system300 includes a mechanism that reads information on the dish (i.e.,barcode or RFID) and directs the specimen to the incubator (or theassigned incubator if more than one).

The sample container enters the incubator cabinet in integratedincubator and image capture module 3 through a first door 310 onto shelf320 where a robotic arm (not shown) catalogs the specimen by reading acode thereon and places it on an available shelf in the incubator for aprescribed incubation time. The location of the sample container in thecabinet is associated with the sample for later retrieval of the sample.

The prescribed incubation time may be set by a lab operator.Alternatively, the incubation time may be pre-set based on certaindiscrete inputs such as the amount and type of sample, the targetmicroorganism(s), the culture media, etc. In this regard, the incubatorincludes a processing unit (not shown) that cooperates with the roboticarm to inventory the sample containers as they enter the incubator.

The processing unit is not described in detail herein. Such units forthe inventory and monitoring of samples in a cabinet type of incubatorfor incubation of large number of samples in containers are well knownto the skilled person and not described in detail herein. Such automatedsystems may include one or more processors or other dedicated logic andmemory for storing and tracking information related to the samplecontainers in the incubator. In this regard, the processing unit tracksat least the location of the specimen in the incubator, the incubationtime, the number of images to be captured, the number of times thespecimen is to be imaged and duration therebetween. The duration betweenthe time a specimen is imaged, replaced back into the cabinet andremoved again for imaging is referred to herein as an “imaginginterval.” However, one of ordinary skill in the art will appreciatethat the processing unit may track additional information, such as thetype of sample, the type of culture media, precautionary handlinginformation (i.e., hazardous specimens), etc.

Information related to the samples may be stored in a database or tablelocated in the memory of the processing unit. The one or more processorswill update the information stored in the memory, accordingly. Forinstance, when a new sample container is received at the first door 310,the one or more processors of the system's processing unit will create anew entry in the database stored in memory. Accordingly, a start timeand end time for the prescribed incubation interval may be set. Further,in preferred embodiments, the database will schedule the imagingintervals and will include an indication (i.e., timestamp, a check mark,or flag) of when the image has been captured. Alternatively, thedatabase may include blank entries such that the actual time the samplecontainer was imaged can be entered.

Imaging the specimens during the prescribed incubation time can occuronce or, more typically, multiple times at discrete imaging intervals toobtain images of the sample container over time to determine whether ornot cultures of microorganisms are growing in the sample container. Theexamples described herein discuss imaging specimens periodically.However, one of ordinary skill in the art would recognize that thespecimens may be imaged just once (i.e., as they exit the incubator),twice (i.e., as they enter and exit the incubator), or any suitablenumber of times during the incubation period.

In this regard, the robotic arm retrieves the sample container from itsshelf. The sample container is placed on shelf 220 before passing intothe image capture module 200 through door 210. Door 210 is an example ofa portal through which petri dishes are conveyed into and from theimaging module. Door 210 is referred to herein as a third door todistinguish this door 210 from first and second doors for initialingress and final egress of petri dishes into and out of the cabinet. Inthis regard, each of the ports described herein may be configured withone door or with separately controlled doors, one for ingress and onefor egress. For example, the third door 210 may be a dual doorconstruction (e.g., one door for dishes entering the image capturemodule 200 and one door for dishes exiting the image capture module 200)or any other suitable mechanism that limits the exchange of atmospherebetween the incubator and the image capture module. While embodimentsherein describe configurations with at least three doors, the skilledperson will appreciate that the cabinet can be further adapted toinclude additional ports to support additional functions that requirepetri dishes to be removed from and replaced in the cabinet. Such doorscan also be configured to have either single or multiple ports.

The image of the sample container is captured by the imaging unit 230 ofthe image capture module 200. The sample then passes through third door210 back into incubator 100, and onto interior shelf 220 where it isretrieved by the robotic arm and placed on an available shelf.Accordingly, the processing unit of the incubator may select thelocation of the available shelf based on the further processing plannedfor the dish. For example, dishes that require further image processingmay be placed on an available shelf closer to the image capture module.Further, dishes that are nearing the end of their incubation time may beplaced on a shelf near the second door 410.

The location of the sample container in the incubator is updated in thesystem. At any time, based on expiration of time, imaging results, userintervention, or the occurrence of other conditions or events detectedeither by sensors or operator observations, the sample container may bemoved to the exit as discussed below.

As discussed above, the processing unit of the incubator will cooperatewith the robotic arm and the image capturing system 200 to update theinformation in the database. Thus, when the image of the samplecontainer is captured by the imaging unit 230, the processing unitreceives an indication or notification that the image has been captured.The one or more processors of the processing unit will then update theimage information related to the sample in the database.

One of ordinary skill in the art would recognize that image capture canoccur at intervals defined by the operator, such as hourly, every sixhours, once (i.e., after incubation), twice (i.e., entering theincubator and exiting the incubator), etc. In the alternative, theimaging intervals may be predetermined and associated with the samplecontainer itself in the data base. Specifically, the nature of thesample, the media in which the sample is placed, or the targetmicroorganism may be useful in determining how long to incubate thesample and the time intervals between image capture of the sample. Forexample, it may be determined that an interval of at least, e.g., sixhours must elapse before the first signs of microbial growth might bedetected by the imaging apparatus. In this example, when the robot firstreads the bar code affixed to the sample container, the system recordsthat the sample container is to be removed from the incubator and sentto the imaging module for imaging in six hours. When the six hours haveelapsed, the robot retrieves the sample container and places it on theshelf 220 for it to be conveyed from the cabinet and into the imagingmodule. Furthermore, a skilled artisan will appreciate that certainsamples may be incubated for more or less time as appropriate and mayneed to be imaged with greater or less frequency than other samples. Forinstance, a sample with an incubation time of twelve hours may be imagedevery thirty minutes, whereas a sample with an incubation time ofthirty-six hours may be imaged once an hour. Alternative incubationtimes and imaging intervals are a matter of choice on the part of theoperator of the system. Suitable incubation times and imaging intervalsare readily determined by one skilled in the art.

When the prescribed incubation time has expired or the sample isrequested by a lab operator, the robotic arm retrieves the samplecontainer from its location in the incubator cabinet and places thesample container on the cabinet shelf that supports the conveyor thatconveys samples from the cabinet for removal therefrom through seconddoor 410. The sample container passes through the second door 410 andexits the incubator where it can be retrieved by a lab operator forfurther analysis, sent for disposal, or sent for further analysis in anautomated manner (e.g., a module or instrument engaged with the cabinetvia a track or conveyor system).

In this regard, the processing unit may update the informationassociated with the sample container/sample in the database memoryindicating that the sample container/sample has exited the incubator.That is, the processing unit may indicate that the sample specimen hascompleted its prescribed incubation time or is ready for furtherprocessing. Thus, the processing unit may store the entry for apredetermined amount of time after the sample specimen has completed itsprescribed incubation time. Alternatively, the processing unit mayforward the completed entry to a third-party where it could be storedfor later retrieval.

Although the invention has been described as being used in an automatedlab setting, alternative embodiments allow for a lab operator tomanually feed specimens in to and receive incubated specimens from theintegrated incubator and imaging module 1. Accordingly, the first tracksystem 300 and the second track system 400 need not be present inalternative embodiments. In other embodiments, different conveyorconfigurations may be used when a lab operator provides the samplecontainers to the incubator system manually. Such track systems arewell-known to one skilled in the art and will not be described in detailherein.

Turning to FIG. 5A, an example of a storage array 18 is shown. Asdiscussed above, the storage arrays 18 line the inner walls of theincubation chamber 5. FIGS. 5A and 5B also show the waste removal outlet35 that may be included in some embodiments. According to thoseembodiments, the waste removal outlet 35 may be a port that is sealableby a door or shutter 37, which allows a waste container 2 c to beremoved from the incubation chamber 5. Door or shutter 37 may beclosable to prevent access into the incubation chamber 5. Themicroprocessor 10 may control the opening and closing of the door orshutter 37. In some embodiments, the door or shutter 37 may include asensor (not shown) to detect the presence of the robotic arm or acontainer 2. In this regard, the door or shutter 37 typically opens whena sensor detects the presence of the robotic arm 20 or a container 2.Although described in the context of the operation of the door orshutter 37, all doors of the integrated incubator and imaging module canbe operated in the described manner.

When included in the incubation chamber, the waste removal outlet 35 maybe provided in a side of the incubation chamber 5 other than the side inwhich the first door 7 and the second door 9 are located. In someembodiments the waste removal outlet 35 may be located on a wallopposite of the first door 7 and the second door 9. As shown in FIG. 5A,the incubation chamber 5 is provided with a door 38 which is hinged 39to the housing 4 for allowing access to the interior of the incubationchamber 5 and the waste removal outlet 35 may be provided in the door38. Alternatively, the waste removal outlet 35 may be provided on a walladjacent to the wall with the first door 7 and the second door 9.

Referring to FIG. 5A, the door 38 is illustrated from the interior ofincubation chamber 5. In embodiments that include the waste removaloutlet, the storage array 18 may break at the location of the wasteremoval outlet 35. In some embodiments, the container includes a lid.According to these embodiments, the waste removal station may include aseal applicator 39 for applying a seal to the container for sealing thelid to the container to prevent dislocation of the lid from the dish.Typically, the seal applicator may be a tape applicator for applying anadhesive tape around the dish and the lid. In alternative embodiments,the seal applicator may be an applicator to shrink-wrap the container.Alternatively, the seal applicator may apply glue or a heat weld betweenthe lid and the container so that the lid and the dish are fixed to oneanother.

FIG. 5B illustrates the exterior of the door 38. According to someembodiments, door 38 may also include the waste removal outlet 35, whichleads to a waste removal station 36. The waste removal station 36 mayinclude a waste transport element 40 for transporting a waste container2 c from the waste removal outlet 35 to a waste container 41. The wastetransport element 40 may include at least one sterilization component.Accordingly the sterilization component may include a source ofirradiation 61 or a gas source 42 configured to introduce a gas into thewaste transport element 40. Alternatively, a washing and rinsingmechanism may be provided for certain types of containers.

In some embodiments, the waste transport element 40 may be a wasteremoval chute. However, FIG. 5B illustrates a waste removal tube 40 tomore reliably prevent contamination. The waste removal tube 40 mayinclude two sealable waste doors 43 and 44 with associated motoroperated drives 43 a and 44 a. The motor operated drives 43 a and 44 acontrol doors 43 and 44, respectively, and allow a waste container 2 cto pass there through. In this regard, the doors 43 and 44 are opened instages to prevent access into an upstream part of the waste removal tube40.

In embodiments that include the waste removal outlet, the waste removalstation 36 may also include a pressure generator. For example, the gassource 42 may generate an overpressure in the waste removal tube 40between the two sealable waste doors 43 and 44. Alternatively, the gassource 42 may reduce pressure in the waste container such that the airwill flow from the environment to the waste container. In this regard,no contaminated air can escape from the waste container, therebyprotecting the environment from contamination.

According to some embodiments, the waste container 41 is removable. Inthis regard, the waste container 41 attaches to the waste transportelement 40, for example, by means of a bayonet connection. Theconnection means may be arranged such that upon removing the wastecontainer 41 from the waste removal tube 40, the tube 40 isautomatically closed off by a sealing door. Preferably, a double sealingdoor 45 is provided to seal off the door. When a new waste container 41is connected to the tube, the sealing door 45 is arranged to openautomatically.

In the embodiments that include the waste removal outlet, the wasteremoval station 36 may include at least one counter 46 for countingcontainers 2 c removed from the waste removal outlet 35. This allows thewaste removal station 37 to track the correct removal of containers andto provide an indication when the waste container 41 is expected to befull.

In alternative embodiments, a reader 26 maybe be proximately located tothe waste removal outlet 35 to keep track of the containers 2 c.Typically, the waste container 41 is configured to be mobile to be movedbetween integrated incubator and image capture modules 3. For examplethe waste container 41 may be provided with wheels 47 or any suitablemeans for transporting the waste container 41 between the integratedincubator and image capture modules 3.

Although the embodiments described herein refer to a waste removal tube40 through which the cell culture devices are passed under the influenceof gravity, a more controlled removal of waste containers can berealized in alternative embodiments. For example, the waste transportelement may include a motor configured to operate a waste removalconveyor, such as an elevator or stacker. The microprocessor 10 maycontrol the waste removal conveyor to control the discharging wastecontainers from the waste removal outlet to the waste container.

In other embodiments, the waste removal outlet may be omitted from thedoor 38. Accordingly, the microprocessor 10 may direct the robotic arm20 to discharge the container 2 c via the second door 9. In this regard,the robotic arm may remove container 2 c from its shelf and place it onthe shelf to be transferred to the second track system. The container 2c may then traverse the second track system 400 until reaching a sortingunit (not shown). Accordingly, the sorting unit may route the container2 c to a disposal area. Alternatively, the sorting unit may direct thecontainer 2 c to a rack where the containers can be disposed of by a labtechnician.

FIGS. 7A and 7B illustrate front view and side views of the integratedincubator and image capture module 3, with the imaging module disposedon what is designated the front of the cabinet. The illustratedconveyers 300 and 400 allow the integrated incubator/imaging module 3 tobe incorporated in an automated lab setting. As described above, thefirst track system 300 includes a first door 310 where samplecontainers, such as petri dishes and other specimen containers, enterthe incubator. First track system 300 interconnects with a series ofother tracks or other automated lab equipment to allow for the movementof petri dishes through the automated lab. Although the sample containeris described as a petri dish in the description of the severalembodiments herein, the skilled person will appreciate that theapparatus described herein is readily adapted to handle other types ofsample containers.

FIGS. 7A and 7B illustrate the image capture module 200 as placed nearthe top of the integrated incubator image capture module 3. The petridishes are conveyed from the cabinet and through door 210 via theconveyor supported by shelf 220. The petri dishes are returned to thecabinet through the same door 210 via the conveyor supported by shelf220. In this regard, the door 210 is configured to allow the samplecontainer (e.g. petri dish) to be conveyed through it when opened, butis not significantly larger than the sample container to minimize lossof controlled atmosphere from the cabinet when the door is opened.

Furthermore, image capture module 200 is a contained unit immediatelyadjacent the incubator that keeps the door 210 separated from theambient laboratory atmosphere.

In preferred embodiments, image capture module 200 includeshigh-efficiency particulate absorption (HEPA) filters to keepcontaminants that are present in the lab ambient atmosphere fromcontaminating the samples conveyed to and from the image capturemodule/incubator cabinet. In alternative embodiments, other devices maybe used to prevent contaminants from entering the image capture module200, such as UV lights or a series of filters with varying degrees ofgranularity. One of ordinary skill in the art would recognize that thecontaminant prevention mechanisms described herein may be used on theirown or in combination with other filtering equipment.

Preferred embodiments of the image capture module 200 may also includeinsulation to reduce heat loss from the incubator environment to thelaboratory atmosphere through the image capture module 200.Alternatively, the image capture module 200 includes seals to furtherreduce the extent to which the lab atmosphere might enter the imagecapture module and contaminate the sample containers conveyed therethrough or enter into the incubator as the sample containers aretransferred from the incubator to the image capture module. Thus, theimage capture module 200 incorporates the use of filters and insulatingmaterials to reduce contamination of the sample containers during imagecapture.

FIGS. 7A and 7B also illustrate door 410 where petri dishes and otherspecimens exit the incubator onto the second conveyor system 400. It isimportant to note that doors 210, 310, and 410, located on the face ofthe incubator, are configured to permit sample containers to beautomatically conveyed in and out of the incubator cabinet. Therefore,these doors or ports are substantially smaller in size than a doorlocated on another side of the cabinet that allows operator access tothe interior of the cabinet. Such a large door can be disposed on anyside of the cabinet. In preferred embodiments, the size of the doors isslightly bigger than the size of a petri dish and is largely a matter ofdesign choice. As noted above, it is preferred that the doors be nolarger than necessary to keep the interior environment of the incubatoras stable as possible as sample containers are conveyed in and out ofthe cabinet. Alternative embodiments contemplate door sizes that areapproximately 1½ inches high by 3 inches wide.

FIG. 8 shows an example of a conveyor module 4320 that serves totransport sample containers (petri dishes are illustrated). In variousconfigurations, the conveyor module 4320 can feed sample containers bothinto and out of the incubator cabinet through doors 310 and 410. In thecontext of the first conveyor system 300, conveyor module 4320 has aconveyor system 40 that can cooperate with other conveyors to convey thepetri dishes among the various stations in the automated lab. Conveyingsystems such as those illustrated herein are well known to one skilledin the art and are not described in detail herein. Adjacent to conveyorsystem 40 is a device (no shown), such as a bar code scanner or RFIDreader, for reading identification data in the form of a bar code on thepetri dishes that are conveyed by the conveyor module 4320. One ofordinary skill in the art would recognize that alternative devicereaders/identification tags could be used in place of a bar code scanneror the RFID reader.

When a bar code on a petri dish is read by the scanner or reader and thesystem determines that the petri dish is to be directed from the cabinetof the integrated incubator and image capture module 3 a signal is sentto switching mechanism 30 to direct the petri dish from the assignedcabinet. In this regard, switching mechanism 30 diverts the selectedpetri dish from incubator door 10 to the conveyor system 40. The petridish passes through the door 10 from the incubator shelf 20, where thepetri dish is catalogued by a reader (e.g. a bar code reader, RFIDreader, etc.) which communicates with a processor to update theprocessor on the location of the petri dish.

In the context of the second conveyor system 400 (FIGS. 7A-B), therobotic arm (not shown) is directed to place the petri dish on shelf 420when the processor has determined that the petri dish has completed itsprescribed incubation time or is requested by a lab operator or isindicated to be ready for downstream processing. In this regard, theprocessor may advantageously update information related to the petridish with respect to the further processing of the petri dish. That is,the incubation system may advantageously communicate with othercomponents of the automated lab, and in particular the conveyor system,to indicate further processing of the petri dish. As noted above, thesystem contemplates full automation in delivering samples to theincubator, transporting and storing them in the incubator, temporarilyremoving the petri dishes to the imaging system, returning the samplesto the incubator for further growth and subsequent further inspectionand transporting the petri dishes from the incubator for furtherprocessing, inspection or disposal. Conveyors and other mechanisms forconveying petri dishes to and from the incubator are well known to oneskilled in the art and not described in detail herein

With reference to FIG. 8, in one embodiment of those aspects of thesystem where the petri dish is conveyed from the cabinet, the conveyor,supported by shelf 20 conveys the petri dish through door 10 ontoconveyor module 4320. The switching mechanism 30 directs the petri dishonto the main portion of the conveyor system 40. The conveyor system forboth conveying petri dishes toward the cabinet and away from thecabinet, shown in FIGS. 1, 2A, and 2B, are configured such that thepetri dishes do not collide or otherwise interfere with one another asthey are being transported.

Once the petri dish is on the conveyor module 4320 it may be transporteddownstream for further processing. Typically, the incubated petri disheswill be conveyed to a stacking conveyor system module as discussed ingreater detail below. In some embodiments, the incubated petri dishesmay be conveyed downstream for further processing, such as inoculating adifferent media with the cell growth, tracking the size of the colony,enzyme detection, etc. Other downstream processing techniques would bereadily apparent to those skilled in the art and are not discussed infurther detail herein.

Additionally, the conveyor system may transport incubated petri dishesto a disposal area. Typically, when no culture growth has been detectedby either the imaging analysis unit or the lab operator or both, theplate may be conveyed to the disposal area. The disposal area may alsobe a stacking system as described in greater detail below, where petridishes are retrieved by a lab operator and disposed of accordingly.Alternatively, petri dishes may be advantageously conveyed to abiohazard waste receptacle.

FIG. 9 illustrates a stacking conveyor system module 350 that connectsto conveyor module 4320. Stacking conveyor system 350 has a conveyorsystem 440 (as described above with respect to FIGS. 1, 2A, 2B) thatruns in a direction parallel to the direction of conveyor system 40 ofconveyor module 4320. Stacking conveyor system 350 has a series of racks370 that store petri dishes in stacks disposed in the racks. AlthoughFIG. 9 illustrates four racks 370A, 370B, 370C, and 370D, one ofordinary skill in the art would appreciate that the stacking conveyorsystem 350 can have more or fewer racks.

In operation, petri dishes are conveyed along conveyor system 440. Inthis regard, the system comprises a plurality of dish stopping units(not shown). The system tracks the progress of the dish through theconveyor system. Therefore, when a petri dish is determined by thesystem to be beneath the appropriate rack (the particular rack selectedwill depend on why the petri dish was removed; e.g., for furtherprocessing, disposal, etc.), the system sends signals that will causethe petri dish to be loaded into one of the racks 370A, 370B, 370C, or370D. To accomplish this, the conveyor system 440 is provided with amechanism that places the petri dish into its assigned rack. The racks370A, 370B, 370C, and 370D include a one-way gate that allows petridishes to pass into the racks and holds them in the rack to prevent themfrom falling back onto conveyor system 440. In preferred embodiments,the racks 370A, 370B, 370C, and 370D can hold up to 20 petri dishes.Stacking dishes significantly higher than 20 creates a greater risk ofthe dishes toppling, which would ruin the sample, create a contaminationrisk, etc.

The stacking conveyor system 350 automates sample container collectionfrom the integrated incubator and image capture module 3 or any othersuitable automated lab equipment, for example an automated inoculationsystem such as the one described in US Provisional Patent ApplicationNo. 61/973,551 filed on Apr. 1, 2014 and entitled “System and Method forthe Automated Preparation of Biological Samples” which is commonlyassigned with the present application and hereby incorporated byreference. Using the stacking conveyor, sample containers can becollected in predetermined order and stacked in such order for retrievalby a lab operator. Such automated tools reduces the amount to which theinterior of the cabinet needs to accessed, thereby preserving theenvironment inside the cabinet.

In some embodiments, one of the racks 370A, 370B, 370C, or 370D may bededicated to receiving plates for disposal. As discussed above, platesthat did not exhibit culture growth, or were otherwise defective, may becollected in one of the dedicated racks to be disposed of by the laboperator in a safe manner or disposed through the waste door 37 aspreviously described.

Alternatively, the processor 10 may send signals to the conveyor systemto convey the incubated dish for further downstream processing. Asdiscussed above, this may include inoculating other media with theculture growth, image analysis of the plate, enzyme analysis, etc.Additionally, the conveyor system may automatically direct the incubatedplates to an automatic disposal unit (not shown).

The housing for the image capture module 200 is shown in FIG. 10. Imagecapture module 200 housing has a transparent portion 290 that permits alab operator to view the operation of the image capture module 200.Additionally, the housing has filters 280 disposed therein to preventcontaminants from entering the interior portions of the image capturemodule 200. As discussed above, the filters 280 are preferably HEPAfilters. However, the filters 280 may be a series of filters, one ofwhich may be a HEPA filter, or UV lights that neutralize contaminants.One of ordinary skill in the art would recognize that any suitablefilter capable of capturing contaminants from entering the module orescaping therefrom could be used. Furthermore, a skilled artisan wouldrecognize that the filter mechanisms described herein could be usedindividually or in combination.

Referring to FIGS. 11-16, the image capture module 200 is shown withpetri dishes passing through in various stages of being imaged. Asdiscussed above, a petri dish is transported through door 210 and intothe image capture module 200. As illustrated in FIG. 11, the petri dishtravels along conveyor system 240. The petri dish reaches a location itis read by a reader (i.e. bar code scanner or RFID reader). The petridish is then placed back on the conveyor system 240, where it then movesthe dish onto rotating carousel tray 255. The lid manipulator 250subsequently removes the lid of the petri dish. Rotating carousel tray255 moves the petri dish into position under image capture unit 230,which will be described in further detail below.

Once an image of the petri dish is captured by image capture unit 230,the rotating carousel tray 255 rotates the dish to a post-processingposition. In the post-processing position, the lid is replaced on top ofthe petri dish and the petri dish is placed on conveyor system 245. Theconveyor system 245 returns the petri dish to the shelf 220 in incubator100 through door 210. Once on the shelf 220, the petri dish label isread and the robotic arm, in response to instructions from theprocessor, retrieves the petri dish and places the petri dish on anavailable shelf to continue incubation, with the system updated with thelocation of the petri dish in the cabinet, or relocated to the exitmechanism if the system is so instructed. As discussed above,information regarding the placement and processing history of the petridish as it is transported through the image capture module is maintainedin the processing unit of the incubator.

The movement of the petri dish through the image capture module 200 isillustrated in FIGS. 12A and 12B. At position 2100, the robotic armplaces the petri dish (not shown) that has been selected for imaging onshelf 220. In position 2150, the petri dish is conveyed through door 210by way of the conveyor 240 of the image capture module 200. The conveyor240 moves the petri dish to location 2250 where it is rotated andcatalogued by a reader (e.g. bar code or RFID). The petri dish is thenrotated and moved on conveyor 240 to location 2300, where the lidmanipulator unit 250 removes the lid from the petri dish. The rotatingcarousel tray 255 then moves the petri dish into position under theimage capture unit 230. The image capturing unit 230 captures a digitalimage of the petri dish at location 2350. Equipment for the capture ofdigital images of plated cultures is well known to one skilled in theart and is not described in detail herein.

At location 2350, the integrated incubator and image capture module 3optionally displays the captured digital image of the cultured sample ona display (not shown) for review. The processing unit may also save theimage electronically. Devices for storing digital information, e.g.,servers, storage systems and devices, memory devices, etc. are wellknown to one skilled in the art and not described in detail herein. Inalternative embodiments, the digital image is analyzed using a softwareprogram that can determine, based on prior information/images of thepetri dish if microbial growth has occurred. Such programs for digitalinspection of the culture to detect changes indicative of microbialgrowth are known to the skilled person and not described in detailherein. Once such program is described in US Provisional PatentApplication No. 61/933,426 filed on Jan. 30, 2014 and entitled “A Systemand Method for Image Acquisition Using Supervised High Quality Imaging”which is commonly assigned with the present application and herebyincorporated by reference. Upon automatic digital inspection of thecaptured image the processor can alert a lab operator of anyabnormalities, such as rapid culture growth or other anomalies.Additionally, the captured image may be displayed for the lab operator'sreview at the appropriate time along with prior images of the plate forvisual comparison by the operator in addition to or as a substitute fordigital analysis of the captured image using the digital image analysis.

Once the digital image of the plated culture is captured by the imagingunit at location 2350, the rotating carousel tray 255 carries the petridish to the post-processing phase at location 2400. At location 2400 thelid is placed back on top of the petri dish and transferred to conveyorsystem 245. The conveyor system 245 conveys the petri dish to door 210at location 2550. There, the petri dish is conveyed through door 210 andonto shelf 220. There the petri dish tag is again read, and theprocessor controls the incubator's robotic arm 20, at location 2600, toretrieve the petri dish and place it on an available shelf, or move itto the exit mechanism if so instructed. The location of the petri dishis updated in the system. The petri dish continues to reside at thislocation while further incubating for its prescribed incubation time. Asdiscussed above, information regarding the status of the petri dish asit passes through the image capture module and back into the incubatorcabinet is continually updated so that the information regarding thestatus and analysis of the petri dish and the plated culture within thedish is continuously updated by the system using the central processingunit of the incubator.

Referring to FIG. 13, the lid manipulator unit 250 is shown in greaterdetail. The lid manipulator unit 250 includes an arm 2520 that moves amanipulator unit 2510 vertically. The manipulator unit 2510 is loweredover a lid of the petri dish by the arm 2520 until it makes contact withthe lid of the dish. The manipulator unit 2520 then lifts the lid offthe dish using a suctioning pad. The dish is subsequently loaded intothe rotating tray 255 for image processing. Optionally, both the lid andthe dish are tagged so that the lid can be accurately replaced onto itsrespective dish after imaging. Placing the wrong lid on the petri dishcan result in cross contamination.

In some embodiments, there is a second lid manipulator unit forreplacing the lid on top of the petri dish after the image processing instep 2400. However, the same lid manipulator unit may be used to removeand replace the lid on the petri dish before and after image processing.The lid manipulator unit 250 is not described in detail herein, and theskilled person will appreciate that this function can be performed in avariety of ways. In one embodiment the lid manipulator unit includes atleast one motor that moves the manipulator into a position where it canboth remove and replace the lid. In other embodiments, the lidmanipulator 250 may be driven by a pneumatic system or any othersuitable means for moving the manipulator to its intended locations.

In one embodiment the manipulator unit 2510 is a suctioning device. Inalternative embodiments, manipulator unit could include a claw, a hook,or any other suitable means for lifting off and replacing a lid on thecontainer or receptacle (e.g. the petri dish) without disturbing thegrowth of the cultures.

Turning to FIG. 14, the rotating carousel tray 255 that transports thedish into position for image capture is shown. In preferred embodiments,rotating carousel tray 255 has two available receptacles 25510A and25510B that receive petri dishes. Additionally, the rotating carouseltray includes a pneumatic cylinder 25520 to drive the rotating carouseltray 255. Alternatively the rotating carousel tray may be driven by amotor. Further, the rotating carousel includes a shelf 25530 thatsupports the image capture unit 230.

The receptacles 25510A and 25510B help to streamline the process ofloading and off-loading the petri dishes for image capture. Although theillustrated embodiment describes two receptacles, one of ordinary skillin the art would recognize that the rotating carousel tray 255 may haveany number of receptacles depending on the size of the sample containersand the imaging module.

In operation, a petri dish is loaded into one of the receptacles 25510.In the illustrated embodiment, there are two receptacles 25510 eachwhich can receive one petri dish, one being loaded and one beingunloaded. Alternative embodiments contemplate the use of more than tworeceptacles. For example, one plate may be loaded into the carousel tray255 for image processing while another plate is being removed from thecarousel tray 255 after being photographed; a third plate may be locatedunder the image capturing unit 230; and the last plate may be in aholding position, either waiting to be photographed or just having itsphotograph taken.

The pneumatic cylinder 25520 drives the rotation of the carousel tray255. That is, the pneumatic cylinder 25520 moves the receptacles 25510into locations where the dishes can be placed into or removed from areceptacle. Moreover, the pneumatic cylinder 25520 rotates the carouseltray 255 such that petri dishes may be photographed by image captureunit 230. In this manner the dishes rotate through the image processingsteps discussed above with respect to FIG. 12.

FIG. 15 shows one embodiment of an image capture unit 230. Image captureunit 230 includes an image sensor unit 2310, a lens unit 2320, at leastone light source 2330, and a channel 2340 for lids to pass.Alternatively, the image capture unit 230 may not include a channel2340.

In one embodiment, the image sensor 2310 is a high-resolution imagesensor, such as a charge-coupled device (CCD). However, any suitableimage sensor may be used, including CMOS or NMOS image sensors. Suchsensors are well known to one skilled in the art and are not describedin detail herein. While only one image sensor unit 2310 is shown in FIG.15, one of ordinary skill in the art would recognize that several imagesensor units, of varying types, may be used. In this regard, multipleimages may be captured from a variety of positions or angles. Further,images may be captured at different wavelengths.

Image capture unit 230 also includes a lens 2320. In one embodiment, thelens is a 16 millimeter lens. However, one of ordinary skill wouldrecognize that any suitable lens could be used in conjunction with theimage sensor 2310. Such lenses are well known to those skilled in theart and are not described in detail herein.

Additionally, image capture unit 230 has at least one light source 2330.The light source directs light to illuminate the sample containers forimage capture. In preferred embodiments, the light source 2330 is one ormore light emitting diodes (LEDs). In certain embodiments, wavelengthsof light are selected to provide an image across the visual spectrum.Any suitable light source may be used to illuminate the petri dish forimage capture. In some embodiments, light source 2330 has at least threeindividual light sources that emit at the same or different wavelengthranges. It is contemplated that any number of light sources may be usedto provide illuminating light suitable for imaging the cultures.Illuminating light can be directed onto the sample from a variety ofdirections which are largely a matter of design choice, depending upon,among other things, the orientation of the image capture apparatus andother optics of the system. In alternate embodiments, the light source2330 may be located above, to the side, or beneath the petri dish toilluminate the petri dish for image capture. In other embodiments, thelight is directed onto the sample from multiple different directions.Accordingly, the light source 2330 may be included that illuminates thepetri dish from both above and below to provide the appropriate amountof light so that the image capture unit can capture an image of thespecimen

In some embodiments, the lid manipulator 250 will remove the lid 2302from the dish 2301. The dish 2301 will then be placed into one of thereceptacles 25510 of the carousel tray 255. As discussed above, thecarousel tray 255 will convey the dish through image processing.Meanwhile, the lid manipulator 250 is moving dish 2301's lid over thecarousel tray 255, through the channel 2340, and to the location wherethe lid will be placed back on dish 2301. In this regard, channel 2340allows for linear movement of the lid to its final destination, therebyproviding the most efficient and direct route to replacing the lid backon the dish.

Referring to FIG. 16, an exemplary embodiment of the light source 2330is shown. In preferred embodiments, the light source 2330 has severalLEDs 2335. The LEDs 335 are arranged as a dodecagon with six groups oftwo LEDs each (i.e., twelve rectangular white LEDs total). In oneembodiment, the LEDs are operated in groups of two, so that light may becontrolled from six different directions. However, arrangements of LEDsto obtain the desired imaging are largely a matter of design choice.Suitable alternative geometric LED arrangements include hexagonal,octagonal, circular, triangular, and square arrangements.

In other embodiments, the light source 2330 is configured to beconnected to the image capture unit 230 in such a way that it directslight to the sample container from either one direction or a variety ofdirections. As noted above, the image capture unit 230 may also includea light source that is above, to the side, or beneath the petri dish toilluminate the dish. In other embodiments, the light source may beincluded that illuminates the petri dish from both above and below toprovide the appropriate amount of light so that the image capture unitcan capture an image of the specimen.

In preferred embodiments, the light source 2330 has a center aperture2340 through which the image of the petri dish is captured by thecamera. In this regard, the camera is mounted at a certain distance fromthe petri dish based on a variety of factors, such as opticaldistortion, reflection of the light source, etc. The aperture allows thecamera to be positioned at a predetermined distance from the petri dishwithout the LED plate blocking the camera's angle of view.

Although the invention herein has been described with reference toparticular embodiments, it is to be understood that these embodimentsare merely illustrative of the principles and applications of thepresent invention. It is therefore to be understood that these andvarious other omissions, additions, and numerous modifications may bemade to the illustrative embodiments and that other arrangements may bedevised without departing from the spirit and scope of the presentinvention as defined by the appended claims.

1-24. (canceled)
 25. A method for incubating and monitoring biologicalsamples disposed in culture media in an integrated system for incubatingand monitoring biological samples disposed in culture media, the methodcomprising: conveying a sample container into an incubator comprising acabinet with multiple sealable ports for automated receipt and removalof sample containers from the cabinet, wherein the cabinet includes afirst sealable port, a second sealable port, and a third sealable port,wherein the first, second, and third sealable ports are verticallyspaced apart on a single face of the cabinet; maintaining a controlledtemperature environment and a controlled atmosphere composition for thesample containers stored in the cabinet; receiving, through the firstsealable port, sample containers from a first conveyor adapted tocooperate with the first sealable port to receive sample containerscontaining biological samples inoculated with a sample for incubationinto the cabinet; receiving, through the second sealable port, samplecontainers from a second conveyor that conveys sample containers fromthe cabinet; conveying sample containers from the cabinet through thethird sealable port via an image capture conveyor in an image capturemodule disposed in a housing separate from the cabinet, conveying thesample containers from the image capture conveyor to a rotatingcarousel, wherein the rotating carousel has a plurality of receptacles,each for receiving a sample container; and wherein the rotating carouselmoves the sample container from a location where the sample container isreceived by the rotating carousel, to an image capture position of animaging unit in the image capture module wherein the imaging unitcomprises an image sensor, a lens and a light source; obtaining an imageof a biological sample in the sample containers at the image captureposition; and conveying the sample containers from the rotating carouselto the image capture conveyor and through the third sealable port to thecabinet after the image capture module obtains the image of a biologicalsample in the sample containers, wherein the third sealable port is anonly port into the image capture module from the cabinet, and furtherwherein the first, second and third sealable ports are sealable byfirst, second and third doors.
 26. The method of claim 25, wherein thethird sealable port further comprises: a sealable ingress port adaptedto receive sample containers into the image capture module from thecabinet prior to imaging of the sample containers; and a sealable egressport adapted to transport sample containers from the image capturemodule to the cabinet after imaging of the sample containers.
 27. Themethod of claim 25 further comprising automatically opening a door thatsealably closes the first sealable port when the first conveyer conveysa sample container to the first sealable port for placement in thecabinet.
 28. The method of claim 25 wherein the integrated system forincubating and monitoring biological samples further comprises aprocessor configured to control conveying the sample containers withinthe cabinet and through the first, second, and third sealable portsaccording to instructions communicated to the processor.
 29. The methodof claim 28 wherein the integrated system for incubating and monitoringbiological samples further comprises a memory in communication with theprocessor, wherein the memory receives information related to placementof the sample container in the cabinet and provides such information topermit the sample container to be located in the cabinet for processing.30. The method of claim 29 further comprising at least one of: i)receiving sample containers conveyed through the first sealable port andplacing them in an available location in the cabinet for subsequentretrieval; ii) removing sample containers from their location in thecabinet and placing them at the second sealable port to be conveyed fromthe cabinet; iii) removing sample containers from their location in thecabinet and placing them at the third sealable port to be conveyed fromthe cabinet for image capture; iv) receiving sample containers at thethird sealable port subsequent to image capture and placing them backinto an available location in the cabinet; or v) transporting samplecontainers from a first position in the cabinet to a second position inthe cabinet.
 31. The method of claim 30 wherein the integrated systemfor incubating and monitoring biological samples further comprises arobotic arm, in communication with the processor and the memory,comprising a gripper and a translation arm for gripping and movingsample containers for performing at least one of: i) receiving samplecontainers conveyed through the first sealable port and placing them inan available location in the cabinet for subsequent retrieval; ii)removing sample containers from their location in the cabinet andplacing them at the second sealable port to be conveyed from thecabinet; iii) removing sample containers from their location in thecabinet and placing them at the third sealable port to be conveyed fromthe cabinet for image capture; iv) receiving sample containers at thethird sealable port subsequent to image capture and placing them backinto an available location in the cabinet; or v) transporting samplecontainers from a first position in the cabinet to a second position inthe cabinet.
 32. The method of claim 25, wherein the image capturemodule is adjacent to the incubator and outside the cabinet.
 33. Themethod of claim 25 further comprising: automatically removing a lid fromthe sample container prior to image capture of the sample container,wherein the integrated system for incubating and monitoring biologicalsamples further comprises a lid manipulator unit comprising an arm themethod further comprising moving the lid manipulator unit vertically,the lid manipulator unit comprising a suction pad.
 34. The method ofclaim 33, further comprising placing a lid onto the sample containerafter image capture of the sample container without the lid thereonusing the lid manipulator unit.
 35. The method of claim 25 furthercomprising illuminating the sample container for image capture using alight source.
 36. The method of claim 35, wherein the light sourcecomprises at least one light emitting diode (LED).
 37. The method ofclaim 25, further comprising: sorting a plurality of sample containersaccording to pre-programmed categories after being removed from theincubator, wherein the sorting is performed by a stacking conveyorsystem, wherein the stacking conveyor system comprises a series ofracks.